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Chromosome Replication02:31

Chromosome Replication

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Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins.  This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin...
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Replication in Eukaryotes01:29

Replication in Eukaryotes

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In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
Many Proteins Orchestrate Replication at the Origin
Eukaryotic replication follows many of the same...
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Replication in Eukaryotes02:31

Replication in Eukaryotes

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Overview
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Chromosome Structure02:40

Chromosome Structure

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A functional eukaryotic chromosome must contain three elements: a centromere, telomeres, and numerous origins of replication.
The centromere is a DNA sequence that links sister chromatids. This is also where kinetochores, protein complexes to which spindle microtubules attach, are constructed after the chromosome is replicated. The kinetochores allow the spindle microtubules to move the chromosomes within the cell during cell division.
Telomeres consist of non-coding repetitive nucleotide...
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The Nucleosome Core Particle01:12

The Nucleosome Core Particle

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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
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The Nucleosome Core Particle02:10

The Nucleosome Core Particle

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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
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Updated: Mar 11, 2026

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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Nucleosome occupancy as a novel chromatin parameter for replication origin functions.

Jairo Rodriguez1, Laura Lee1,2, Bryony Lynch1

  • 1Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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Summary

Nucleosome occupancy around DNA replication origins in G1 phase is crucial for regulating origin activation time and efficiency. Proper establishment of this chromatin feature is essential for genome-wide replication control.

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Area of Science:

  • Cell Biology
  • Genetics
  • Molecular Biology

Background:

  • Eukaryotic DNA replication initiates from multiple origins of replication.
  • Origin activation requires precise regulation of pre-replicative complex (pre-RC) assembly and firing.
  • Chromatin structure is known to influence DNA replication, but specific parameters remain unclear.

Purpose of the Study:

  • To investigate the role of chromatin parameters, specifically nucleosome occupancy, in regulating DNA replication origin activity.
  • To determine how nucleosome occupancy around origins affects their firing time, efficiency, and pre-RC formation.
  • To elucidate the mechanism by which nucleosome occupancy is established and its impact on global origin usage.

Main Methods:

  • Analysis of nucleosome occupancy variation around origins of replication in Saccharomyces cerevisiae.
  • Correlation analysis between nucleosome occupancy and origin firing characteristics (time, frequency).
  • Investigation of pre-RC formation and cell-cycle dependent nucleosome occupancy changes in wild-type and mutant strains (orc1-161).

Main Results:

  • Nucleosome occupancy in G1 phase varies significantly around origins and correlates with activation time, efficiency, and pre-RC formation.
  • Nucleosome occupancy around origins is established during the G2/M to G1 transition in a pre-RC-dependent manner.
  • Disruption of cell-cycle dependent nucleosome occupancy changes (orc1-161 mutant) leads to abnormal global origin usage.

Conclusions:

  • Nucleosome occupancy is a novel and key chromatin parameter that regulates DNA replication origin activity.
  • Proper establishment of nucleosome occupancy around origins is critical for controlling global origin usage and ensuring accurate genome replication.
  • This study provides new insights into the interplay between chromatin structure and the regulation of DNA replication initiation.